The code to make the directories should not be performed in a method that is meant to return a descriptor to the framework. It should be done in "setup", that's the proper place where everything related to preparing a work directory is supposed to happen.

Actually I double checked, the on-disk invoke struct is created during 'cluster_commands()' so that's the method you need to override instead of setup().

So do I keep old version (with minor improvements in variable names and plus of course), or should I avoid altering the command line and created subfolders directly instead?

Don't modify the command line. Just writ the ruby code that run the mkdir. That's it.

ok. Another possibility is to factor out invocation struct massaging into separate method, so setup can be used

Done.

(adjusted to create subfolders asap)

As agreed in person with Pierre, the method cluster_commands() is modified (but in a more complex way than at the first attempt)